Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

(2019) Pavel Neumann et al.   Mobile DNA

Non-Robertsonian translocations involving chromosomes 13, 14, or 15 in male infertility

(2019) Hongguo Zhang et al.   MEDICINE

CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture

(2019) Kunling Chen et al.   Annual Review of Plant Biology

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Genome evolution, structural rearrangements and speciation

(2017) P. G. D. Feulner et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes

(2017) Haomin Lyu et al.   NEW PHYTOLOGIST

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Recursive random forest algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways

(2017) Wenping Deng et al.   PLoS One

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

(2016) Jeanine L. Olsen et al.   NATURE

Plant metabolic clusters - from genetics to genomics

(2016) Hans-Wilhelm Nützmann et al.   NEW PHYTOLOGIST

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

(2016) Zhen Li et al.   PLANT CELL

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

(2015) Ting Xie et al.   Molecular Plant

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome sequence of the orchid Phalaenopsis equestris

(2014) Jing Cai et al.   NATURE GENETICS

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Ecological and evolutionary significance of genomic GC content diversity in monocots

(2014) Petr Šmarda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

(2013) Rajinder Singh et al.   NATURE

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Banana Genome Hub

(2013) Gaëtan Droc et al.   Database-The Journal of Biological Databases and Curation

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Domain enhanced lookup time accelerated BLAST

(2012) Grzegorz M Boratyn et al.   Biology Direct

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

The flowering world: a tale of duplications

(2009) Yves Van de Peer et al.   TRENDS IN PLANT SCIENCE

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE